Tuesday, February 06, 2018

How many lncRNAs are functional?

There's solid evidence that 90% of your genome is junk. Most of it is transcribed at some time but the transcripts are transient and usually confined to the nucleus. They are junk RNA [Functional RNAs?]. This is the view held by many experts but you wouldn't know that from reading the scientific literature and the popular press. The opposition to junk DNA gets much more attention in both venues.

There are very few serious reviews that address the controversy over function (but see Palazzo and Lee, 2015 ... the figure is from their paper). That's why I want to highlight a review that's just been published in Cell. It's a review that recognizes the controversy over function and points to the possibility that most putative lncRNAs may be junk (Kopp and Mendell, 2018). I'm going to quote directly from the introduction and the conclusion to show you how scientific reviews are supposed to be written.

There is a broad range of estimates for the number of lncRNA genes in mammals, ranging from less than 20,000 to over 100,000 in humans. Nevertheless, the function and biological relevance of the vast majority of lncRNAs remain enigmatic. Given that transcriptional regulatory elements, such as enhancers and promoters, are now known to initiate transcription bi-directionally, it is likely that many lncRNAs—if not the majority—actually represent RNAs that initiate at enhancers or promoters but do not perform sequence-specific functions. This conclusion is further suggested by the fact that many lncRNAs are localized to the nucleus with low expression levels and little primary sequence conservation. Recent reports of local gene regulation by lncRNA loci reinforce this notion and suggest that in many cases, the act of transcription or DNA elements within the lncRNA locus are more likely to be the source of regulatory activity than the actual lncRNA itself. Given these observations, it is clear that the mere existence or production of an RNA does not automatically imply its functionality. Indeed, we must assume until proven otherwise that of the tens of thousands of annotated lncRNAs, those that function independently of the DNA sequence from which they are transcribed represent a small minority. Nevertheless, even if a small percentage of lncRNAs are functional, they would still constitute a major gene class with hundreds or possibly thousands of members.

The best available data shows that less than 500 putative lncRNAs have a well-defined function. When I'm calculating the amount of functional DNA in the human genome I usually assume 5,000 genes for noncoding RNAs—most of them are not lncRNAs. I still think that's a good estimate.

The act of transcription around promoter regions may play a role in regulation. In such cases, the sequence of the transcript may be irrelevant but the transcribed region of the genome has a function. There aren't very many proven examples of this type of function. In most cases it looks like the transcripts are just due to sloppy initiation. Kopp and Mendell make an important point in the introduction when they say that the mere existence of a transcript does not mean it has a function. This point is usually ignored in the scientific literature.

The authors reinforce this view in their conclusions. They emphasize a point that most scientists find awkward; namely, that the default assumption must be lack of function (junk RNA) and the burden of proof is on those who propose that most lncRNAs have a function. When we detect a transcript, the most we can say for certain is that there's a transcription initiation site nearby. It may or may not be important.

Over the last decade, the study of lncRNAs has stimulated vigorous debate over the question of whether noncoding RNAs represent “transcriptional noise” or truly functional biomolecules. Clearly, there is no unifying answer—meaningful understanding of lncRNA function (or lack thereof) can only be achieved from detailed study on a case-by-case basis. Importantly, our evolving understanding of the prevalence of genomic elements that produce noncoding transcripts, such as enhancers, has mandated that we approach the experimental evaluation of a lncRNA locus with an agnostic view regarding whether the produced RNA is functional. As Occam’s razor dictates, the simplest hypothesis, in this case that the production of a lncRNA most likely marks the presence of a regulatory DNA element, is often the correct one.

I'm pleased to see that more and more scientists are recognizing the very real controversies over junk DNA and the role of pervasive transcription. Unfortunately, it still takes a bit of courage to stand up to the dominant (but incorrect) paradigm promoted by the ENCODE publicity campaign over the past decade.

6 comments
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Tonegawa is confident that the very existence of physical links between neurons stores memories. But other researchers have their own notions.

Back in the 1950s, McConnell suspected that RNA, cellular material that can help carry out genetic instructions but can also carry information itself, might somehow store memories.

This unorthodox idea, that RNA is involved in memory storage, has at least one modern-day supporter in Glanzman, who plans to present preliminary data at a meeting in April that suggest injections of RNA can transfer memory between sea slugs.

Glanzman thinks that RNA is a temporary storage vessel for memories, though. The real engram, he suggests, is the folding pattern of DNA in cells’ nuclei. Changes to how tightly DNA is packed can govern how genes are deployed. Those changes, part of what’s known as the epigenetic code, can be made — and even transferred — by roving RNA molecules, Glanzman argues. He is quick to point out that his idea, memory transfer by RNA, is radical. “I don’t think you could find another card-carrying Ph.D. neuroscientist who believes that.”

Other researchers, including neurobiologist David Sweatt of Vanderbilt University in Nashville, also suspect that long-lasting epigenetic changes to DNA hold memories, an idea Sweatt has been pursuing for 20 years. Because epigenetic changes can be stable, “they possess the unique attribute necessary to contribute to the engram,” he says.

Long before the advent of single-cell RNA-Seq, highly-precise spatial organization of lncRNAs had been observed by in situ hybridization, which showed that the expression of many lncRNAs is restricted to individual brain regions, structures, or cell types (Figure IC) [15].

Consistent with previous studies [2, 14], the brain, testis, lung and skin tissues have more TS lncRNAs and TS protein coding genes, perhaps due to the presence of heterogeneous cell types in these tissues or from a need for more diverse lncRNA repertoires. Interestingly, the high number of TS lncRNA in testis has been discovered by several previous studies [9, 10, 13]. Both our study and Cabili et al. found that the testis tissue has the highest number of TS lncRNAs across the tissues considered, and 36.5% TS lincRNAs are also detected by Cabili et al., which is significant. Thus, testis-specific lincRNAs may define a new class of RNAs in this organ. These results might be because this organ may represent a breeding ground for new genes, and may be due to the particularly efficient activity of proto-promoters in testis cells [9, 15]. Many TS lncRNAs are also found in other tissues. For example, two TS lncRNAs of the pancreas tissue, CTD-2503O16.4 (ENSG00000249856) and LINC00511 (ENSG00000227036) have been uncovered to be high-confidence human islet-cell genes [16]. On the contrary, the number of TS lncRNAs is lower in the breast, muscle and adipose tissues, reflecting more specialized functions of these tissues. In addition, we found that the TS lncRNAs overlap with those identified by Cabili et al. based on the K-means clustering with the tissue specificity distance measure (Supplementary Table S3).

I expected this to be the molecular level intelligence brain that goes from one thought to the next through time, by reproducing/renewing itself each time via reproduction. Quick illustration again:

LncRNAs are in my opinion essentially RNA based components needed for self-assembly of networked brain circuits, for the part of us that's billions of years old. I expect the answer to just how smart the molecular level brain actually is will be even more amazing, but making a connectome for the entire innards of reproductive cells makes the (still years away) full connectome for the giant brain in our cranium seem easy.

Hopefully you can at least agree that with lncRNA research making visible progress towards finding a useful function it's necessary that they make as fast as possible progress towards wherever that goes, or else we're all stuck waiting longer than is necessary for them to get there.

Laurence A. Moran

Larry Moran is a Professor Emeritus in the Department of Biochemistry at the University of Toronto. You can contact him by looking up his email address on the University of Toronto website.

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Quotations

The old argument of design in nature, as given by Paley, which formerly seemed to me to be so conclusive, fails, now that the law of natural selection has been discovered. We can no longer argue that, for instance, the beautiful hinge of a bivalve shell must have been made by an intelligent being, like the hinge of a door by man. There seems to be no more design in the variability of organic beings and in the action of natural selection, than in the course which the wind blows.Charles Darwin (c1880)Although I am fully convinced of the truth of the views given in this volume, I by no means expect to convince experienced naturalists whose minds are stocked with a multitude of facts all viewed, during a long course of years, from a point of view directly opposite to mine. It is so easy to hide our ignorance under such expressions as "plan of creation," "unity of design," etc., and to think that we give an explanation when we only restate a fact. Any one whose disposition leads him to attach more weight to unexplained difficulties than to the explanation of a certain number of facts will certainly reject the theory.

Charles Darwin (1859)Science reveals where religion conceals. Where religion purports to explain, it actually resorts to tautology. To assert that "God did it" is no more than an admission of ignorance dressed deceitfully as an explanation...

Quotations

The world is not inhabited exclusively by fools, and when a subject arouses intense interest, as this one has, something other than semantics is usually at stake.
Stephen Jay Gould (1982)
I have championed contingency, and will continue to do so, because its large realm and legitimate claims have been so poorly attended by evolutionary scientists who cannot discern the beat of this different drummer while their brains and ears remain tuned to only the sounds of general theory.
Stephen Jay Gould (2002) p.1339
The essence of Darwinism lies in its claim that natural selection creates the fit. Variation is ubiquitous and random in direction. It supplies raw material only. Natural selection directs the course of evolutionary change.
Stephen Jay Gould (1977)
Rudyard Kipling asked how the leopard got its spots, the rhino its wrinkled skin. He called his answers "just-so stories." When evolutionists try to explain form and behavior, they also tell just-so stories—and the agent is natural selection. Virtuosity in invention replaces testability as the criterion for acceptance.
Stephen Jay Gould (1980)
Since 'change of gene frequencies in populations' is the 'official' definition of evolution, randomness has transgressed Darwin's border and asserted itself as an agent of evolutionary change.
Stephen Jay Gould (1983) p.335
The first commandment for all versions of NOMA might be summarized by stating: "Thou shalt not mix the magisteria by claiming that God directly ordains important events in the history of nature by special interference knowable only through revelation and not accessible to science." In common parlance, we refer to such special interference as "miracle"—operationally defined as a unique and temporary suspension of natural law to reorder the facts of nature by divine fiat.
Stephen Jay Gould (1999) p.84

Quotations

My own view is that conclusions about the evolution of human behavior should be based on research at least as rigorous as that used in studying nonhuman animals. And if you read the animal behavior journals, you'll see that this requirement sets the bar pretty high, so that many assertions about evolutionary psychology sink without a trace.

Jerry Coyne
Why Evolution Is TrueI once made the remark that two things disappeared in 1990: one was communism, the other was biochemistry and that only one of them should be allowed to come back.

Sydney Brenner
TIBS Dec. 2000
It is naïve to think that if a species' environment changes the species must adapt or else become extinct.... Just as a changed environment need not set in motion selection for new adaptations, new adaptations may evolve in an unchanging environment if new mutations arise that are superior to any pre-existing variations

Douglas Futuyma
One of the most frightening things in the Western world, and in this country in particular, is the number of people who believe in things that are scientifically false. If someone tells me that the earth is less than 10,000 years old, in my opinion he should see a psychiatrist.

Francis Crick
There will be no difficulty in computers being adapted to biology. There will be luddites. But they will be buried.

Sydney Brenner
An atheist before Darwin could have said, following Hume: 'I have no explanation for complex biological design. All I know is that God isn't a good explanation, so we must wait and hope that somebody comes up with a better one.' I can't help feeling that such a position, though logically sound, would have left one feeling pretty unsatisfied, and that although atheism might have been logically tenable before Darwin, Darwin made it possible to be an intellectually fulfilled atheist

Richard Dawkins
Another curious aspect of the theory of evolution is that everybody thinks he understand it. I mean philosophers, social scientists, and so on. While in fact very few people understand it, actually as it stands, even as it stood when Darwin expressed it, and even less as we now may be able to understand it in biology.

Jacques Monod
The false view of evolution as a process of global optimizing has been applied literally by engineers who, taken in by a mistaken metaphor, have attempted to find globally optimal solutions to design problems by writing programs that model evolution by natural selection.